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PLU Organic Chemistry Laboratory I (Chem 234)	A COSY NMR Spectrum

Spring 2001 Syllabus for ORGANIC CHEMISTRY LABORATORY II (234)

This Course Accompanies Organic Chemistry I - Chem 232.

Instructor: C. Fryhle
Office: Rieke Science Center 240
Phone: 253-535-8314
Email: fryhle@rainier.chem.plu.edu

Course Materials:

1) Introduction to Organic Laboratory Techniques - A Microscale Approach, Pavia et al, Saunders, 3rd ed., 1999
2) Laboratory Notebook, bound quadrilled carbon-less form type.
3) Lab Safety Goggles

Schedule of Experiments
Open Lab Hours
Laboratory Safety
Laboratory Notebooks
Samples
Weekly Reports
Individual Formal Reports
Laboratory Exam
Academic Policies
Grading

Laboratory Schedule

Week		Date	The Experiments		Questions			Points
NOTE: YOU MUST COMPLETE THE LABORATORY SAFETY TOUR BEFORE PERFORMING ANY BENCH WORK.
I	2/7-2/9			a) Study introductory material in pp. 2-36 NOTE: Laboratory Safety Information, pp. 4-20 b) Introduction to Microscale Laboratory, pp. 38-45
II	2/12-2/16			a) Laboratory Exercise 1, Options A, B, C (p. 46) b) Solubility (Exp. 2, p. 49-60, Parts A-D)		None	40
III	2/19-2/23			Crystallization (Exp. 3, Parts A and B only, p. 60) Report for Parts A and B		1	40
IV	2/26-3/2			Acetylsalicylic Acid (Exp. 8, p. 102) w/ FTIR Essays: "Aspirin" and "Analgesics," pp. 105-109		3,7	40
V	3/5-3/9			Extraction (Exp. 4, p. 71, parts A-D) w/ FTIR Ident. on Part D Essay: "Caffeine," pp. 119-123		Report (A-D)	40
VI	3/12-3/16			Isopentyl Acetate (Exp. 12, p. 131) w/ FTIR and GC Essay: "Esters - Flavors and Fragrances," pp. 128-130		1,2,3,4	40
VII	3/19-3/23			Reactivities of Some Alkyl Halides (Exp. 18, p. 190)		1,3	40
	3/24-4/1			Spring Break
VIII	4/2-4/6			Dehydration of Methylcyclohexanols (Exp. 23A, p. 222) w/ FTIR and GC		1,2,3	40
IX	4/9-4/12			Group Formal Report		Due 4/20	100
X	4/17-4/20			Continue Group Work on Formal Report
				(LAB CLOSED 4/12 and 4/16 for Easter Break)
XI	4/23-4/27			Synthesis and Reactions of cis-5,6-Norbornene-endo-2,3- dicarboxylic Anhydride (Handout) w/ FTIR		Handout	40
XII	4/30-5/4			Stereochemistry - Spearmint and Caraway Oil (Exp. 14, p. 146) w/ NMR, FTIR and GC Essay: "Stereochemical Theory of Odor," pp. 143-146		1,2,3,4	40
XIII	5/7-5/11			An Oxidation-Reduction Scheme: Borneol, Camphor, Isoborneol (Exp. 28, p 266) w/ NMR and IR		1,2,3,5,6	40
XIV	5/14-5/18			Lab Final Exam			60
	5/14-5/18			Notebooks Turned in for Evaluation			40

				TOTAL POINTS			600

Laboratory Safety:

You must complete a Chemistry Department Laboratory Safety Tour before you can begin work in the Open laboratory. You must also read and sign the Department's safety policies sheet, titled "Laboratory Safety", and turn it in at the Stockroom at the end of your safety tour.

Be sure to read Pavia, et al, regarding safety information and precautions that must be taken in the laboratory.
Goggles are required at all times in the laboratory.
Food and drink are prohibited in the Open Laboratory.
Foot apparel must cover your full foot. Open-toe shoes or sandals are not allowed. If you are not wearing proper footwear you will not be allowed to work in the Open Lab.
Material Safety Data Sheets (MSDS) are explained on pp. 9-11 in Pavia. MSDSs for the reagents you will use in each week's experiment are available at the Teaching Station (center) of the Open Lab. MSDSs can also be accessed on-line via the Department of Chemistry Home Page. They should be consulted during the preparation of your prelab report for information about the hazards and properties of the chemicals you will use. It is also helpful to record the Registry Numbers in your notebook for the reagents used.
Disposable gloves are available at the Stockroom window for a small fee. In general, I recommend that you do not use gloves. If you do use gloves, you must remove them before handling any communal items such as balances, reagent bottles, pipets, telephones, door knobs, etc., or else you will contaminate the items you touch and make it unsafe for others not wearing gloves.

The Lab Notebook:

Your notebook should be a complete and continuously updated diary or journal for your work in the laboratory. Your notebook is the only place where notes about your laboratory work should be kept, and it should be a thorough record of your work. A stranger with approximately your level of training should be able to read your notebook, repeat your work without any additional assistance, and obtain results similar to your own. In research and industrial situations, a laboratory notebook is a legal document that is signed daily by the author and frequently by a witness. You should ascribe corresponding importance to your laboratory notebook.

The notebook specified for this course is designed to make carbon-less copies of your notes. Use your notebook for recording ALL of your work in the laboratory.
Use indelible ink for all notebook entries. Pencil or water soluble inks are not acceptible.
Scraps of paper or notes written on loose paper are not acceptable. Faculty in the Open Lab have been instructed to confiscate any notes not written in the specified bound notebook.
You may use the back side of your notebook pages (those pages on the left when the notebook is open) for scratch notes or preliminary ("back of the envelope" type) calculations, etc. when the need arises. These are notes for your use that are not part of the report when it is turned in.
You are not to re-copy lab notes before turning them in. The notebook is to be a living diary of the work you did in the lab at as close to the moment you did it as possible.
If your notebook cover does not provide for a Table of Contents, set aside the first several pages of your notebook to keep a running Table of Contents. Add an entry to the Table of Contents each time you perform an experiment, noting the relevant pages.
Any errors that are made in the notebook should be crossed out by a single line. Errors should not be obliterated by erasing, drawing over, or covering with paper or correcting fluid. It is occasionally the case that what was considered to be an erroneous entry at one time turns out to be correct or valuable and is needed at some later date.
The prelab portion of your report (specified below) must be complete and initialed by the Open Lab instructor before you will be allowed to check equipment out of the stockroom and begin work.
The number of points possible for each experiment is listed above in the Schedule of Experiments table. The Pre-Lab portion of each report is worth 10 points. The In-Lab notes are worth 15 points. Assigned exercises are worth 5 points. When there is a sample produced by an experiment the sample itself is worth 5 points and the properly labeled vial is also worth 5 points. Thus, the maximum possible for most experiments is 40 points. If there are no exercises and/or there is no sample produced then the total possible is reduced by the corresponding amount.

Format for Lab Notes:

Your notebook format should be basically that described in Pavia et al., pp. 21-27. The Pavia model as well as a few additional required sections are listed by the headings below. Be sure to begin the notebook with the Table of Contents, as specified above.

Prelab Portion (10 Points)

Date

Title

Reference (e.g., Pavia et al., Exp. X, pp. YY-ZZ)

Goal or Purpose (brief but descriptive)

Main Reaction [balanced equation(s), including likely side reactions] (Note that this section might not be appropriate for non-preparative experiments. In this case a few brief statement about the work to be done will suffice.)

Table of Relevant Physical Constants or "Reaction Table" Format - MW, mp or bp, density (for liquids), planned weights and moles, actual amounts and moles (the amounts actually used are filled in after the experiment is begun), ratio of moles between reactants (the limiting reagent is used as the lowest common denominator), and Registry Numbers for organic and hazardous inorganic reagents.

Separation Scheme (Usually a flow chart - not a written duplicate of the planned lab procedure copied from the book. - Be concise but complete.) The goal of this section is to show where actual physical separations of materials occur (and what the materials are) as you move through the experiment to obtain a pure, isolated material. See Pavia, et al, pp 24.

HAZARDS (of the chemicals and/or the procedures) In addition to the lab manual, you will need to consult the Material Safety Data Sheets (MSDS's) available on-line (Department of Chemistry Home Page) and in the Open Lab. Registry Numbers can also be listed her , if not noted already included in your Reaction Table. General information on laboratory safety and MSDSs is given in Pavia, et al, pp 1-19.
[All of the above sections must be entered in your notebook
and initialed by the instructor on duty before the Stockroom
will be allowed to issue you your equipment.]

Prelab Portion (10 Points)
Date Title Reference (e.g., Pavia et al., Exp. X, pp. YY-ZZ) Goal or Purpose (brief but descriptive) Main Reaction [balanced equation(s), including likely side reactions] (Note that this section might not be appropriate for non-preparative experiments. In this case a few brief statement about the work to be done will suffice.) Table of Relevant Physical Constants or "Reaction Table" Format - MW, mp or bp, density (for liquids), planned weights and moles, actual amounts and moles (the amounts actually used are filled in after the experiment is begun), ratio of moles between reactants (the limiting reagent is used as the lowest common denominator), and Registry Numbers for organic and hazardous inorganic reagents. Separation Scheme (Usually a flow chart - not a written duplicate of the planned lab procedure copied from the book. - Be concise but complete.) The goal of this section is to show where actual physical separations of materials occur (and what the materials are) as you move through the experiment to obtain a pure, isolated material. See Pavia, et al, pp 24. HAZARDS (of the chemicals and/or the procedures) In addition to the lab manual, you will need to consult the Material Safety Data Sheets (MSDS's) available on-line (Department of Chemistry Home Page) and in the Open Lab. Registry Numbers can also be listed her , if not noted already included in your Reaction Table. General information on laboratory safety and MSDSs is given in Pavia, et al, pp 1-19. [All of the above sections must be entered in your notebook and initialed by the instructor on duty before the Stockroom will be allowed to issue you your equipment.]

In-lab Portion (15 Points)

In-lab Notes, Data, and Observations - Written continuously during the lab period documenting your work in your notebook as you do the work, not at some later time or date. Your notes should be sufficient for someone else to duplicate your work, even though your notes may not necessarily be in perfect prose.
Interpretation of FTIR, NMR, and GC data - The key identifying or characteristic features of any FTIR, NMR, or GC data should be discussed. Original data from your sample should be attached to the report you turn in for grading.

Calculations - Theoretical yield and actual percentage yield should be given, showing the calculations.

Conclusions - Brief statement or restatement of key results and conclusions. Editorial comments such as "I think the experiment went well.", etc., are not appropriate. Make summary comments on the quality of the product or results, as indicated by the data (including instrumental data if obtained).

Exercises (5 Points)

Date of Completion
Attribution of assistance from others (List the names of other people consulted in the course of your work. See "Academic Policies", below, for further information.)

Your Signature attesting to the honesty and accuracy of your work. Reports will not be graded without a signature.

In-lab Portion (15 Points)
In-lab Notes, Data, and Observations - Written continuously during the lab period documenting your work in your notebook as you do the work, not at some later time or date. Your notes should be sufficient for someone else to duplicate your work, even though your notes may not necessarily be in perfect prose. Interpretation of FTIR, NMR, and GC data - The key identifying or characteristic features of any FTIR, NMR, or GC data should be discussed. Original data from your sample should be attached to the report you turn in for grading. Calculations - Theoretical yield and actual percentage yield should be given, showing the calculations. Conclusions - Brief statement or restatement of key results and conclusions. Editorial comments such as "I think the experiment went well.", etc., are not appropriate. Make summary comments on the quality of the product or results, as indicated by the data (including instrumental data if obtained). Exercises (5 Points) Date of Completion Attribution of assistance from others (List the names of other people consulted in the course of your work. See "Academic Policies", below, for further information.) Your Signature attesting to the honesty and accuracy of your work. Reports will not be graded without a signature.

Reaction Products

(10 Points for Sample and Vial)

Products requiring further work at a later time should be stored in a labeled vial and given to the stockroom assistants for storage. Final products should be labeled as specified on p. 27 of Pavia, et al, with the addition of the date, tare weight of the container and experiment number, and turned in to the stockroom with the specification that they are to be placed in the "To Be Graded" box for the organic lab.

Weekly Reports

The completed lab notes for each experiment, consisting of your work from the prelab through the completed exercises, are due by 2:00 PM on the Monday of the week following a given experiment. Place either the original or carbon-less copy (so long as it is legible) of your lab notes in the appropriate wooden box in the Open Laboratory.

Notebook Spot Checks

In addition, individual lab notebooks may be subject to an unannounced on-the-spot grading once during the semester. This evaluation, worth 20 points, will be part of the overall notebook score and will be used to assess whether the attributes of notebook style specified above are being incorporated. Notebooks will be collected at the end of the semester. If a spot check is done on your notebook (worth 20 points), then grading of your notebook at the end of the term will be worth only 20 points in stead of 40 points.

The Formal Report

The period of April 9-20 is set aside for group preparation of a formal written laboratory report about one of the previously conducted experiments. The formal report will be due April 20 at 5:00 p.m.. Some guidelines for the report are as follows:

Groups of four individuals will collaborate to prepare a single formal report. Experimental data and results will be pooled from within the group to build a substantial work.
The formal report may be written about a single experiment conducted thus far during the semester. To ensure diversity of selected experiments, groups will sign up to write about an experiment on a posted sign-up sheet listing the experiments.
The formal report is to take the form of a full paper to be submitted for publication in a journal of the American Chemical Society, e.g. the Journal of Organic Chemistry or the Journal of the American Chemical Society.
Please refer to the ACS (American Chemical Society) Style Guide, 2nd edition, for details about the format and style expected.
The paper should include the following sections:

Title

Authors Names

Affiliation (Course and Institution address)

Abstract

Introduction

Results and Discussion

Experimental Section

Literature References

Registry Numbers

Group Structure

The four individuals in the group should each take responsibility for one of the following portions of the paper, and then work together to make the paper a cohesive, well-written whole.
The grade for each member of the group will be strongly influenced by the contribution of all the group members, as follows. 80% of the grade for the paper will be the same for all members of the group. Each of the four sections delineated below will be worth 20 points and the score for each section will be summed to achieve 80% of the total. The remaining 20 points of each individual's total score (out of a possible 100) will be calculated by adding again the score for their individual section of the paper.
Collaboration within the group is strongly encouraged, indeed essential. The fundamental thrust of the paper should be agreed upon initially by the group as a whole and relevant data shared. Then, individual group members should prepare drafts of their specific section of the paper. Drafts should then be shared within the group and constructive feedback returned in a timely fashion to the author of each section. All group members should assist with critiquing all sections of the paper. The author of each section should revise their drafts as appropriate, and again solicit feedback from the group. The group should then polish the assembled sections into a finished, very high quality paper, again working through multiple drafts when necessary.
Expectations for the finished paper are very high both in terms of the quality of writing and the level of scientific analysis and literature documentation. You are encouraged to use the library and all other resources available.
The formal report should be typed, double-spaced, and approximately 5-10 pages in length. Be concise, complete, and sure that the paper reads in a logical progression of topics and information.
Each person should prepare their section on a floppy disk in order to facilitate merging of all the contributed parts of the paper.
A variety of computer resources are available for your use in preparing the formal report, including programs for drawing chemical structures and importing them into text documents. See the Organic Chemistry Tool Kit for links and information about some of these. Take advantage of the Computer User Rooms on campus (e.g. in the University Center).
The job assignments and person responsible for each section should be typed at the end of the report. All members of the group should sign the report here, too.

First Individual	Title, Abstract, Registry Numbers, Notation and Format of References	20%
Second Individual	Introduction	20%
Third Individual	Results and Discussion	20%
Fourth Individual	Experimental Section	20%
Individual Score	Individual Section Added Again	20%

The Formal Report is due on April 20 at 5:00 p.m.

Laboratory Final Exam

A Final Exam for the Organic Chemistry I Laboratory (Chem 234) will be self-administered in the Open Lab during the final week of the semester. The exam will be worth 40 points and will cover understanding of organic laboratory techniques, procedures, methods for product analysis, and general laboratory practices. The lab final will be a closed-book test, taken under the spirit of academic honesty, and overseen by the Open Laboratory Faculty Supervisors.

Academic Policies

I expect that all of your work for credit will be done strictly in the spirit of academic honesty. I trust that each one of you will conduct your work with the highest level of integrity. Furthermore, I expect that each of you will assist in maintaining an atmosphere of honesty by bringing to my attention any lapse in academic honesty you observe. Any breach of academic honesty will receive a severe academic penalty. If cheating occurs on any piece of graded work, the minimum penalty will be an automatic grade of zero for that assignment. At the instructor's option a grade of E may be assigned for the entire course. In any case, after an incident of academic dishonesty has occurred a student will not be allowed to withdraw from the course. Falsification of data is a serious offense in research, industrial, and academic settings, and it will be treated as such.

Now with regard to authorized collaboration, it is expected that you will likely discuss experiences about the labs with each other. Each person is to conduct their own experiments, however. Work is to be done individually in the Organic Laboratory. You should feel free to share advice, tips, etc., and make use of the same when you conduct an experiment, but the data you obtain, the notes you write, and the samples you prepare should, of course, be generated by yourself through your own work. You may work with each other when you are answering asigned exercises, much the way you might when you work homework problems. You can learn by helping each other to answer these exercises. However, you must share in the development of answers rather than simply use work done by other individuals. You must give proper credit in your notebook to any person whose input has been utilized.

Grading

Weekly Reports	400 Points
Notebook Check	40 Points
Formal Report	100 Points
Lab Final Exam	40 Points
Grand Total	580 Points

Late reports of all types will be penalized by 10% per day (maximum of half off). Please note that the last day to withdraw from the class and receive a refund is February 21. The last day to file forms for the Pass/Fail option is April 3. The last day to withdraw (no tuition refund) and receive a W grade is May 4. Grade disputes are subject to policies of the Natural Sciences Division.

University Policy

If you need course adaptations or accommodations because of a documented disability, if you have emergency medical information to share with me, or if you need special arrangements in case the building must be evacuated, please make an appointment with me as soon as possible (Rieke 240, X8314), and please contact the Coordinator for Students with Disabilities (Alene Klein, Counseling and Testing Office, Ramstad Hall 106, X 7206). Official notification to the instructor of any disability conditions that may impair a student's academic performance must come from the Coordinator for Students with Disabilities. Without advance warning, such difficulties can not be used later as the basis for requesting make-up course work or reconsideration of grades.

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Last Modified 2/8/00
Copyright 2001, Craig B. Fryhle

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